Yeah, that's the standard method to calculate PCR efficiency. You should believe this method more than curve-fitting methods. You probably did your dilution series wrong.
Some tips:
Vortex vigorously when diluting samples.
Use DNA carrier such as glycerol if your concentrations are low.
Ensure you are measuring Ct's for standard curve between 10 - 30 cycles. Discard results after 30c.
Have your standard curve span at least 5 logs of concentration - i.e. 10e1 to 10e6.
Run in triplicates.

I was also using various curve-fitting models and it was giving me funny values too. Although I like that approach I think it is not robust enough to give you reliable estimation of PCR efficiency. Maybe one day after it will be standardized by some large qPCR cycler manufacturer it will be better.